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- PDB-7ecn: RNA duplex containing C-Ag-A base pairs -

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Basic information

Entry
Database: PDB / ID: 7ecn
TitleRNA duplex containing C-Ag-A base pairs
ComponentsRNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3')
KeywordsRNA / Metal-mediated base pair / Silver
Function / homologySILVER ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKondo, J. / Tsudura, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)24245037 Japan
CitationJournal: To Be Published
Title: RNA duplex containing C-Ag-A base pairs
Authors: Kondo, J. / Tsudura, A.
History
DepositionMar 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3')
B: RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3')
C: RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3')
D: RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7978
Polymers15,3654
Non-polymers4314
Water3,567198
1
A: RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3')
B: RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8984
Polymers7,6832
Non-polymers2162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-19 kcal/mol
Surface area4430 Å2
MethodPISA
2
C: RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3')
D: RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8984
Polymers7,6832
Non-polymers2162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-20 kcal/mol
Surface area4360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.784, 41.482, 45.934
Angle α, β, γ (deg.)90.000, 102.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain
RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3')


Mass: 3841.368 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MOPS, MPD, spermine, potassium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→34.97 Å / Num. obs: 17296 / % possible obs: 99.1 % / Redundancy: 3.278 % / Biso Wilson estimate: 25.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.048 / Χ2: 0.951 / Net I/σ(I): 16.46 / Num. measured all: 56696
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.643.2060.2913.864043128612610.9650.3598.1
1.64-1.693.1890.2284.873942124812360.9880.27599
1.69-1.743.2680.1736.223928120812020.9880.20799.5
1.74-1.793.4030.1747.144056119711920.9780.20799.6
1.79-1.853.4010.1538.323819112611230.9740.18299.7
1.85-1.923.2960.1359.513632111211020.9820.16299.1
1.92-1.993.140.11210.983375107910750.9850.13599.6
1.99-2.073.2320.0913.253332103510310.9920.10899.6
2.07-2.163.4280.07615.233299759710.9940.0999.6
2.16-2.273.4010.06317.9431879449370.9960.07599.3
2.27-2.393.3910.05919.8230899179110.9950.07199.3
2.39-2.533.1560.04522.6926078278260.9970.05499.9
2.53-2.713.260.04224.4826318168070.9970.0598.9
2.71-2.933.4250.03428.6325387477410.9990.0499.2
2.93-3.213.3560.02433.07228969868210.02897.7
3.21-3.583.0690.02434.2318786306120.9990.02997.1
3.58-4.143.1380.02335.8117015525420.9990.02798.2
4.14-5.073.3310.02539.3215724724720.9990.03100
5.07-7.173.0190.02436.4911083713670.9990.02998.9
7.17-34.973.1070.01940.2364021220610.02397.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→34.97 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2034 1721 9.99 %
Rwork0.1696 15500 -
obs0.173 17221 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 38.48 Å2 / Biso mean: 19.9479 Å2 / Biso min: 11.19 Å2
Refinement stepCycle: final / Resolution: 1.6→34.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1016 4 198 1218
Biso mean--21.36 27.19 -
Num. residues----48
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.650.29131420.22711265140797
1.65-1.70.25031400.19641281142198
1.7-1.760.24441430.18411281142499
1.76-1.840.29571420.191512841426100
1.84-1.920.23271460.18651302144899
1.92-2.020.22491430.179112951438100
2.02-2.150.21731440.181812831427100
2.15-2.310.2451440.18361306145099
2.31-2.540.20321440.177913081452100
2.54-2.910.22721450.18511287143299
2.91-3.670.16621390.16951273141296
3.67-34.970.15671490.12731335148499

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